Freshwater Protected Area Resourcbook

4.2 Threatening processes

Globally, freshwater ecosystems are amongst the most threatened of any ecosystem class – and Australia is no exception.Threats to aquatic ecosystems are many and varied, existing over different time and spatial scales. Some can be understood and controlled by simple means, while others are extremely complex and exceptionally difficult to manage (eg: the effects of introduced species). Understanding and managing threats is important to all attempts, within and outside protected areas, to conserve the natural values of aquatic ecosystems.
Within protected areas, the control of threatening processes is central to effective management. As the name implies, protected areas are essentially about protecting identifies values at specific sites from threats.
State threatened species statutes generally seek to control threatening processes. For example, both the NSW Threatened Species Conservation Act, and the NSW Fisheries Management Act allow the identification of Key Threatening Processes (KTPs). KTPs listed to date include changes to natural flow regimes, barriers to movement imposed by in-stream structures, and the degradation of riparian vegetation. Similarly, the Victorian Flora and Fauna Guarantee Act 1988 provides for the designation of Potentially Threatening Processes.
Threats to freshwater ecosystems are discussed in a variety of references, including the 1996 State of the Environment Report (refer also to the Report's technical background papers), and wetland strategies and policies developed by States (see those listed under References). Biodiversity reports and strategies are additional sources of summary information (see for example Government of New Zealand 2000). Allan & Flecker (1993) provide a global perspective on threats to running water ecosystems. Major problems affecting rivers, wetlands and aquifers are detailed below (not in order of importance).
Australian landscapes are generally ancient, formed by erosion and deposition by wind and water over long periods of time. These processes are mediated by vegetation. The alteration of surface flows will alter both erosive forces and the mediating effects of vegetation.
Many terrestrial, aquatic and subterranean ecosystems are groundwater-dependent. Ecosystems most heavily dependent on groundwater include the ecosystems of groundwater-fed rivers, lakes, springs and wetlands, and their immediate terrestrial environments. Groundwater-based ecosystems include aquifers of various kinds, as well as ecosystems in the immediate layers underlying streams, lakes and estuaries.
A variety of threats impact inland aquatic ecosystems. Broadly, the most important are: (a) introduced species, (b) extraction and regulation of water flow for human use, and (c) land use changes in catchments which affect aquatic habitat, or have direct effects on aquatic species. Over-harvest of aquatic organisms can be a major threat, although this is a lesser problem in Australia compared with some other nations. Threats are discussed below under the following headings:

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  extraction of surface or groundwater flows
  
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  stream regulation, agricultural drainage and levee banks
  
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  habitat degradation from other activities
  
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  water pollution
  
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  invasive species
  
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  structures impeding life-cycle journeys, and
  
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  impacts from mining operations.
  

4.2.1 Extraction of surface or groundwater flows

Australia is the world's driest inhabited continent (the driest being Antarctica), and rainfall over much of the land is highly variable. In the two centuries since European occupation, fresh water (both surface and ground) has often been a scarce commodity, and (generally speaking) supplies have been extensively harvested and allocated for human use in the more fertile and more highly populated parts of Australia. For example, if all existing water allocations in the Murray-Darling Basin were used in a single season, around 90% of the average natural stream flow of the catchment would be diverted⁶⁶. The lower Murray now experiences drought-level flows three years out of every four, compared to one in twenty years under natural circumstances⁶⁷. In spite of over-allocation of the water resource, the Murray-Darling Basin Ministerial Council has had difficulty implementing a cap on water usage⁶⁸. The cap was set at 1994 extraction levels, and may not be sufficiently restrictive to protect the remaining biodiversity of many of the Basin's rivers and wetlands⁶⁹. In the Queensland and Victorian sections of the basin, harvesting of overland surface flows with off-stream dams continues to be unregulated by State governments, although these flows should shortly come under State controls as new water legislation is implemented.
Pristine aquatic ecosystems adapt to the flows which are available, even when these flows are highly variable. Removing flows from natural ecosystems will affect them. The more flow removed, the greater the effect; however these relationships are complex, and almost never linear. The timing of the removal is also critical. Both acute and chronic effects may be difficult to understand and predict. Highly mobile animals will be less affected than animals and plants having very limited mobility. Highly water-dependent life forms will be more affected than those of lower dependence. The principles and science of environmental flows seek to minimise the amount of degradation caused by the removal of a certain amount of water; nevertheless the removal of significant water from an aquatic ecosystem will inevitably degrade its natural values.
Removal of water may cause an aquatic ecosystem to dry up, with subsequent obvious changes to both plants and animals. Other effects are more subtle: many native fish, reptiles and birds depend on natural floods as a stimulus for breeding. Without warm, shallow, rising floodplain waters, breeding does not occur (refer to papers by Kingsford).
As mentioned above, many Australian rivers draw their flow from groundwater most of the time. Prior to recent water reforms, groundwater and surface waters were managed with little coordination, and the legacy of this mistake remains today⁷⁰. In some locations around Australia, groundwaters have been so heavily used that springs have dried up, along with their associated local ecosystems. Groundwater pollution with salt or chemical wastes, and changes to aquifer flow patterns, have destroyed or degraded substantial localised freshwater ecosystems⁷¹. At present, State water agencies appear to be using arbitrary rules in allocating groundwater flows to groundwater dependent ecosystems (Murray et al. 2003:112); the use of such approaches, which lack evaluation and assessment mechanisms, appears bound to lead to environmental degradation.
Ecosystems typically supporting short-range endemic taxa (eg. many groundwater systems and mound springs) are of special concern. Biodiversity in some Western Australian aquifers is high by world standards (Humphreys and Harvey 2001). Several discharge springs from the Great Artesian Basin (GAB) and some other aquatic ecosystems are listed as ‘threatened ecological communities’ under the EPBC Act – another protective mechanism albeit not very effective at present. While in theory the EPBC Act can protect against new developments which may constitute a major threat to an area’s values, it cannot force proactive biodiversity management, and it cannot control a multitude of widespread activities draining water flows from a site. Many GAB springs, known to include endemics (Ponder 2004) are already extinct as a result of drawdown resulting from over use of artesian water.
The proliferation of farm dams across catchments alters catchment hydrology, diverting surface flows before they enter watercourses.

4.2.2 Stream regulation, agricultural drainage, and levee banks

These three activities, commonly associated with the development of land for agriculture, can cause massive degradation of river habitat.
Ecological processes in running waters are controlled and constrained by all components of the water regime⁷². The interaction between the water regime and biological processes occurring within a given aquatic environment is extremely complex and, for the most part, poorly understood⁷³. However, it is known that over-regulation of flows by water infrastructure development has caused degradation of many ecological, geomorphological and other physical attributes in Australian rivers⁷⁴. High summer flows in rivers which normally carry low summer flows can interfere with the life-cycles of native plants and animals. In Redgum forests, for example, seed germination occurs during such low flow periods when the floodplain can dry out.
Large dams are often designed to obtain discharge water from the base of the dam, where the water is cold and may be anoxic. Surface discharge mechanisms, as they need to accommodate a changing surface level, are more expensive. The demonstrated effects of cold water pollution include loss or depletion of native warm-water fish species for a number of reasons, such as failure to breed, loss of eggs and juveniles, slower growth and movement speed; and changes to the invertebrate fauna.
Wetlands have been extensively drained, cleared and grazed for agriculture. Overall, around 50% of Australia’s wetlands have been converted to other uses⁷⁵. In some areas the situation is much worse: for example, less than 4% of wetlands in the south-east of South Australia remain, and about 1% in the Greater Adelaide Metropolitan Region. In New South Wales, the Macquarie Marshes, arguably one of the most important wetlands in the southern hemisphere for waterbirds, is among many major wetlands to be seriously degraded⁷⁶. Because wetlands store and slowly release water over time, their loss has further accentuated the highly variable natural flows in unregulated rivers. The temporal and spatial mosaic of ecosystem types in the landscape are important for the protection of biodiversity. Freshwater biodiversity depends in part on the natural diversity of wetland types in the landscape, a pattern which is degraded by draining and damming and the replacement of a range of wetland types by a homogeneous landscape of farm dams⁷⁷.
Levee bank construction has impeded the natural flow of floodwaters over floodplains, reducing the winter replenishment of floodplain wetlands and billabongs in the southern part of the Australian continent.

4.2.3 Habitat degradation stemming other activities

Many of the degrading effects of land use on freshwater ecosystems are linked to poor coordination between government programs, and the short term management priorities of private landholders. Threatening processes include:

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  drainage, land levelling, infilling or channelisation for agricultural purposes;
  
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  alteration of flooding patterns by the construction of levee banks, and the removal of connecting links feeding floodplain wetlands;
  
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  degradation of riparian vegetation by grazing and altered fire regimes;
  
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  changed river morphology associated with erosion and sediment deposition: deep holes, for example, provide drought refuge, yet their existence is dependent on occasional very high flood flows which may be eliminated by dams;
  
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  the alteration of catchment hydrology through the construction of large numbers of farm dams;
  
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  groundwater ecosystem matrix removal (eg. river gravels and groundwater calcretes);
  
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  recreational activity impacts, including over-harvesting, destruction of vegetation, destructive litter such as nylon fishing lines, and poisoning of soils and biota with lead shot;
  
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  the bow wash from powerboats and jetskis erodes banks and uproots aquatic vegetation, while boat noise disturbs wildlife;
  
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  reduction of habitat provided by submerged woody debris by river de-snagging programs;
  
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  disturbance of wildlife and habitat by urban encroachment, including the effects of urban pets; and
  
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  predation and habitat modification by feral animals such as pigs cats, foxes, and dogs.
  

Unconstrained grazing and trampling by introduced herbivores continues to degrade riparian zones over 70% of the continent⁷⁸.

4.2.4 Water pollution from agricultural, urban and industrial sources

Water pollution may be categorised into seven broad classes (not in order of importance):

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  sand and silt, which smother aquatic habitats;
  
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  suspended solids, or other pollutants causing increased turbidity, which inhibit light penetration and thus photosynthesis;
  
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  salt, which causes direct toxicity, and alters ecosystems by favouring salt-adapted species;
  
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  nutrients, which alter ecosystem balances, and can result in algal blooms with toxic and/or oxygen depletion effects;
  
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  industrial and agricultural chemicals, such as pesticides, which can cause acute or chronic toxicity;
  
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  acid resulting from the disturbance of acid-sulphate soils, reasonably common along flat low-lying coastal areas of NSW and southern Queensland. Acid mine drainage may result from similar chemical processes where pyrites are exposed to gaseous or soluble oxygen; and
  
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  thermal pollution, which is usually associated with dams or powerstations. Cold water pollution is discussed above. Powerstations can discharge heated water from cooling systems. In both cases, temperature changes can have acute (eg: death) or chronic (eg: interference with breeding stimuli) effects on downstream ecosystems.
  

4.2.5 Invasive species

The effects of invasive species are pervasive, and generally difficult to manage.
Introduced fish, such as carp, plague minnow (Gambusia sp.) and trout dominate ecosystems in many Australian streams. In New Zealand, re-stocking of rivers in national parks has ceased, and, while angling is permitted, native fish must be returned to the water. Re-stocking of streams with introduced trout continues in Australia. According to Cowx & Collares-Pereira (2002) "stock enhancement programs are a much used and frequently abused management activity".
Carp have proved well adapted to many Australian streams, where they dominate at the expense of native species. In tropical Australia, cane toads (like carp, toads breed rapidly and have indiscriminate appetites) have reduced populations of native frogs and small fish, and present insurmountable removal problems. Cane toads and carp are still expanding their range in Australia.
Exotic riparian vegetation with seasonal leaf-falls (eg. willow) has had a significant impact on rural streams across southern Australia⁷⁹. Many native river ecosystems depend on leaf fall as a key energy input, but this leaf litter needs to enter the ecosystem fairly regularly to enable populations of dependent micro-organisms and invertebrates to maintain stable populations. The highly concentrated leaf fall of the introduced willow overloads the capacity of the stream ecosystems, resulting in a build-up of organic matter whose decay can seriously reduce dissolved oxygen.
The following comments in the New Zealand Biodiversity Strategy apply equally to Australia:

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  most freshwater ecosystems have been significantly modified by introduced species;
  
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  many animal and plant pests are highly invasive in freshwater environments, but are not detected until the extent of their spread makes them difficult to control;
  
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  effective technologies for control or eradication are not always available;
  
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  policies, responsibilities and accountabilities for containing the spread of already established introduced freshwater species that have the potential to become serious pests are not fully developed, and
  
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  illegal transfer and release of aquatic species creates significant risks to indigenous freshwater biodiversity” (Government of NZ 2000:49).
  

4.2.6 Structures impeding the passage of fish on life-cycle journeys.

Most native fish are highly mobile and many require the ability to travel great distances to complete life history stages⁸⁰. The introduction of water infrastructure (especially dams and weirs) in Australia and New Zealand has removed or seriously decreased access for many fish species to areas essential for life history stages⁸¹.
Even when fishways are constructed, they may provide access only for certain species, and often only provide safe access in one direction (upstream). Moreover, such structures may become completely ineffective if poorly maintained or operated.
Freshwater turtles and crayfish may also be adversely affected by dams and weirs. Some turtle and crayfish species are also highly restricted, appearing only in one or two river systems. Many aspects of turtle and crayfish ecology are in urgent need of research. We risk losing species that are undescribed, without knowing their distribution or ecology (N. Chang, University of Queensland, pers.comm. Sept 2002).

4.2.7 Direct and indirect effects of mining operations

Degradation of freshwater ecosystems by mining operations stems from:

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  the mining of materials associated with water systems, such as peat, sphagnum moss, gold, certain gemstones, tin, sand or river gravel;
  
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  water pollution resulting from mining operations, especially sediment, acidic wastes from the oxidation of rocks containing sulphides, and in some cases heavy metal contamination from process wastewaters; and
  
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  altered groundwater regimes resulting from mine dewatering or process water extraction. Perched sand-dune lakes, for example, have been destroyed by sandmining operations which breach and drain groundwater tables. Mines in sedimentary strata can breach, drain and/or connect aquifers at different levels having waters of different history and quality. These effects are seldom well-controlled within current mining operations.
  

4.2.8 Threatening processes: a summary

While all these issues are addressed, in one form or another, by government programs, many of these threatening processes (such as incremental development and exotic pests) are by their nature extremely difficult to deal with. Freshwater ecosystems over much of the Australian continent continue to deteriorate.
Over much of the Australian continent, freshwater ecosystems are either already in crisis, or are rapidly approaching a crisis situation. Introduced plants and animals present huge and intractable problems. The spread of agriculture has been accompanied by grossly excessive wetland drainage and water diversion and extraction. The complex morphology of pristine streams, including deep holes, submerged timber, and gravel and rock beds has disappeared under huge sediment loads from eroding catchments. Grazing of wetlands and riparian areas has destroyed both terrestrial and dependent aquatic ecosystems. Unsustainable levels of water extraction from aquifers has seen the disappearance of springs, wetlands and ephemeral streams. Poorly designed irrigation schemes, and the clearance of deep-rooted vegetation has seen salinity levels rise in streams over large and increasing areas of Australia. Sand mining has destroyed coastal wetlands.
Meanwhile, State water management agencies have, until very recently:

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  issued excessive extraction licences without adequate consideration of environmental flows;
  
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  failed to adopt a strategic approach to the management of the cumulative effects of small to medium-sized water infrastructure developments; and
  
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  adopted a cavalier attitude to the enforcement and auditing of statutory controls⁸² (Nevill 2001, 2003).